SEA-PHAGES | Terminase Genes

Link to this post \| posted 01 Jul, 2018 23:10
gissendanner	According to the bioinformatics guide, there should no more than two terminase genes in the genome–minor subunit and major subunit. Dogfish appears to have three. GP2 is a small subunit gene and GP3 and GP4 appear to be large subunit genes supported by both BLAST and HHPred. This region also has synteny with Nyceirae and Nyceirae is also annotated to have two large terminase subunit genes (3 terminase genes total). Should Dogfish be annotated to have three terminase genes? Thanks Chris

Link to this post | posted 01 Jul, 2018 23:10

According to the bioinformatics guide, there should no more than two terminase genes in the genome–minor subunit and major subunit. Dogfish appears to have three. GP2 is a small subunit gene and GP3 and GP4 appear to be large subunit genes supported by both BLAST and HHPred. This region also has synteny with Nyceirae and Nyceirae is also annotated to have two large terminase subunit genes (3 terminase genes total). Should Dogfish be annotated to have three terminase genes?

Thanks
Chris

Link to this post \| posted 02 Jul, 2018 02:08
gissendanner	After further analysis, GP2 is not well supported to be a small terminase subunit, other than the blast hit to Nyceirae where the same gene is annotated as a small terminase subunit. Both GP3 and GP4 have good support as a large subunit, both from HHpred and Phyre2. Interestingly, GP3 has a coiled-coil domain which is typically found in the small subunit. So, I do not see a small subunit gene and possibly two large subunit genes. Any guidance on the best annotation approach here?

Link to this post | posted 02 Jul, 2018 02:08

gissendanner

After further analysis, GP2 is not well supported to be a small terminase subunit, other than the blast hit to Nyceirae where the same gene is annotated as a small terminase subunit. Both GP3 and GP4 have good support as a large subunit, both from HHpred and Phyre2. Interestingly, GP3 has a coiled-coil domain which is typically found in the small subunit. So, I do not see a small subunit gene and possibly two large subunit genes. Any guidance on the best annotation approach here?

Link to this post \| posted 17 Dec, 2021 14:19
pia1@pitt.edu	This is Ping An at University of Pittsburgh. I'm considering the function calls for genes 2, 3 and 4 of Meyran as terminase, 1 small subunit (gene 2) and 2 large subunits for ATPase domain (gene 3) and nuclease domain (gene 4), respectively. These tentative function calls are consistent with the current consensus for cluster DT phages. But I have some doubts, which seem to echo the two posts above. For gene 2, the best HHpred hit supporting terminase small subunit has a coverage of 45%. For gene 3, the top 5 strongest HHpred hits (probability over 90% and coverage at least 70%) are ATPase. Among these 5, 3 are also nuclease. For gene 4, top 10 strongest HHpred hits (probability over 90% and coverage at least 70%) are nuclease. Among these 10, 3 are also ATPase. Based on the above HHpred analysis, 1. Should gene 2 be assigned the function as “terminase small subunit”? 2. Should gene 3 and 4 be assigned specifically as terminase large subunit (ATPase) and (nuclease), respectively? I hope someone may provide some insights on the issue.

Link to this post | posted 17 Dec, 2021 14:19

pia1@pitt.edu

This is Ping An at University of Pittsburgh. I'm considering the function calls for genes 2, 3 and 4 of Meyran as terminase, 1 small subunit (gene 2) and 2 large subunits for ATPase domain (gene 3) and nuclease domain (gene 4), respectively. These tentative function calls are consistent with the current consensus for cluster DT phages. But I have some doubts, which seem to echo the two posts above.
For gene 2, the best HHpred hit supporting terminase small subunit has a coverage of 45%.
For gene 3, the top 5 strongest HHpred hits (probability over 90% and coverage at least 70%) are ATPase. Among these 5, 3 are also nuclease.
For gene 4, top 10 strongest HHpred hits (probability over 90% and coverage at least 70%) are nuclease. Among these 10, 3 are also ATPase.
Based on the above HHpred analysis,
1. Should gene 2 be assigned the function as “terminase small subunit”?
2. Should gene 3 and 4 be assigned specifically as terminase large subunit (ATPase) and (nuclease), respectively?
I hope someone may provide some insights on the issue.

Link to this post \| posted 17 Dec, 2021 17:45
debbie	Hi Ping, We have seen this before. I would call gene 2 "terminase, small subunit", gene 3 "terminase large subunit (ATPase domain)", and gene 4 "terminase large subunit (nuclease domain)". We have looked into this with the cluster AY phages and worked on a case study to show our investigation. It is still in draft form, but may be helpful. It is attached. 789Kb

Link to this post \| posted 18 Dec, 2021 14:48
pia1@pitt.edu	Thank you! Debbie. That is very helpful.

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Terminase Genes